Jit
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Install HTSLIB on Ubuntu !
By Jit 2222 days ago
➜ Tools git:(master) ✗ wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
--2018-10-25 13:36:41-- https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
Resolving github.com (github.com)... 192.30.253.112, 192.30.253.113
Connecting to github.com (github.com)|192.30.253.112|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/4339773/f2f10d8a-8a73-11e8-89f4-07e1d9d77b17?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20181025%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20181025T113641Z&X-Amz-Expires=300&X-Amz-Signature=2ec8006aeb069dae00035e224e9c2af7b980de816d82672db24e2945fa8aaaf1&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dhtslib-1.9.tar.bz2&response-content-type=application%2Foctet-stream [following]
--2018-10-25 13:36:41-- https://github-production-release-asset-2e65be.s3.amazonaws.com/4339773/f2f10d8a-8a73-11e8-89f4-07e1d9d77b17?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20181025%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20181025T113641Z&X-Amz-Expires=300&X-Amz-Signature=2ec8006aeb069dae00035e224e9c2af7b980de816d82672db24e2945fa8aaaf1&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dhtslib-1.9.tar.bz2&response-content-type=application%2Foctet-stream
Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.216.82.208
Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.216.82.208|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1178859 (1,1M) [application/octet-stream]
Saving to: ‘htslib-1.9.tar.bz2’
htslib-1.9.tar.bz2 100%[===================>] 1,12M 2,20MB/s in 0,5s
2018-10-25 13:36:43 (2,20 MB/s) - ‘htslib-1.9.tar.bz2’ saved [1178859/1178859]
➜ Tools git:(master) ✗ tar -vxjf htslib-1.9.tar.bz2
htslib-1.9/
htslib-1.9/INSTALL
htslib-1.9/LICENSE
htslib-1.9/Makefile
htslib-1.9/NEWS
htslib-1.9/README
htslib-1.9/bcf_sr_sort.c
htslib-1.9/bcf_sr_sort.h
htslib-1.9/bgzf.c
htslib-1.9/bgzip.1
htslib-1.9/bgzip.c
htslib-1.9/config.mk.in
htslib-1.9/configure.ac
htslib-1.9/cram/
htslib-1.9/cram/cram.h
htslib-1.9/cram/cram_codecs.c
htslib-1.9/cram/cram_codecs.h
htslib-1.9/cram/cram_decode.c
htslib-1.9/cram/cram_decode.h
htslib-1.9/cram/cram_encode.c
htslib-1.9/cram/cram_encode.h
htslib-1.9/cram/cram_external.c
htslib-1.9/cram/cram_index.c
htslib-1.9/cram/cram_index.h
htslib-1.9/cram/cram_io.c
htslib-1.9/cram/cram_io.h
htslib-1.9/cram/cram_samtools.c
htslib-1.9/cram/cram_samtools.h
htslib-1.9/cram/cram_stats.c
htslib-1.9/cram/cram_stats.h
htslib-1.9/cram/cram_structs.h
htslib-1.9/cram/files.c
htslib-1.9/cram/mFILE.c
htslib-1.9/cram/mFILE.h
htslib-1.9/cram/misc.h
htslib-1.9/cram/open_trace_file.c
htslib-1.9/cram/open_trace_file.h
htslib-1.9/cram/os.h
htslib-1.9/cram/pooled_alloc.c
htslib-1.9/cram/pooled_alloc.h
htslib-1.9/cram/rANS_byte.h
htslib-1.9/cram/rANS_static.c
htslib-1.9/cram/rANS_static.h
htslib-1.9/cram/sam_header.c
htslib-1.9/cram/sam_header.h
htslib-1.9/cram/string_alloc.c
htslib-1.9/cram/string_alloc.h
htslib-1.9/errmod.c
htslib-1.9/faidx.5
htslib-1.9/faidx.c
htslib-1.9/hfile.c
htslib-1.9/hfile_gcs.c
htslib-1.9/hfile_internal.h
htslib-1.9/hfile_libcurl.c
htslib-1.9/hfile_net.c
htslib-1.9/hfile_s3.c
htslib-1.9/hts.c
htslib-1.9/hts_internal.h
htslib-1.9/hts_os.c
htslib-1.9/htsfile.1
htslib-1.9/htsfile.c
htslib-1.9/htslib.mk
htslib-1.9/htslib.pc.in
htslib-1.9/htslib/
htslib-1.9/htslib/bgzf.h
htslib-1.9/htslib/cram.h
htslib-1.9/htslib/faidx.h
htslib-1.9/htslib/hfile.h
htslib-1.9/htslib/hts.h
htslib-1.9/htslib/hts_defs.h
htslib-1.9/htslib/hts_endian.h
htslib-1.9/htslib/hts_log.h
htslib-1.9/htslib/hts_os.h
htslib-1.9/htslib/kbitset.h
htslib-1.9/htslib/kfunc.h
htslib-1.9/htslib/khash.h
htslib-1.9/htslib/khash_str2int.h
htslib-1.9/htslib/klist.h
htslib-1.9/htslib/knetfile.h
htslib-1.9/htslib/kseq.h
htslib-1.9/htslib/ksort.h
htslib-1.9/htslib/kstring.h
htslib-1.9/htslib/regidx.h
htslib-1.9/htslib/sam.h
htslib-1.9/htslib/synced_bcf_reader.h
htslib-1.9/htslib/tbx.h
htslib-1.9/htslib/thread_pool.h
htslib-1.9/htslib/vcf.h
htslib-1.9/htslib/vcf_sweep.h
htslib-1.9/htslib/vcfutils.h
htslib-1.9/htslib_vars.mk
htslib-1.9/kfunc.c
htslib-1.9/knetfile.c
htslib-1.9/kstring.c
htslib-1.9/m4/
htslib-1.9/m4/hts_prog_cc_warnings.m4
htslib-1.9/md5.c
htslib-1.9/multipart.c
htslib-1.9/os/
htslib-1.9/os/lzma_stub.h
htslib-1.9/os/rand.c
htslib-1.9/plugin.c
htslib-1.9/probaln.c
htslib-1.9/realn.c
htslib-1.9/regidx.c
htslib-1.9/sam.5
htslib-1.9/sam.c
htslib-1.9/synced_bcf_reader.c
htslib-1.9/tabix.1
htslib-1.9/tabix.c
htslib-1.9/tbx.c
htslib-1.9/test/
htslib-1.9/test/auxf#values.sam
htslib-1.9/test/auxf#values_java.cram
htslib-1.9/test/auxf.fa
htslib-1.9/test/auxf.fa.fai
htslib-1.9/test/bgziptest.txt
htslib-1.9/test/bgziptest.txt.gz
htslib-1.9/test/bgziptest.txt.gz.gzi
htslib-1.9/test/c1#bounds.sam
htslib-1.9/test/c1#clip.sam
htslib-1.9/test/c1#noseq.sam
htslib-1.9/test/c1#pad1.sam
htslib-1.9/test/c1#pad2.sam
htslib-1.9/test/c1#pad3.sam
htslib-1.9/test/c1#unknown.sam
htslib-1.9/test/c1.fa
htslib-1.9/test/c1.fa.fai
htslib-1.9/test/c2#pad.sam
htslib-1.9/test/c2.fa
htslib-1.9/test/c2.fa.fai
htslib-1.9/test/ce#1.sam
htslib-1.9/test/ce#1000.sam
htslib-1.9/test/ce#2.sam
htslib-1.9/test/ce#5.sam
htslib-1.9/test/ce#5b.sam
htslib-1.9/test/ce#5b_java.cram
htslib-1.9/test/ce#large_seq.sam
htslib-1.9/test/ce#supp.sam
htslib-1.9/test/ce#tag_depadded.sam
htslib-1.9/test/ce#tag_padded.sam
htslib-1.9/test/ce#unmap.sam
htslib-1.9/test/ce#unmap1.sam
htslib-1.9/test/ce#unmap2.sam
htslib-1.9/test/ce.fa
htslib-1.9/test/ce.fa.fai
htslib-1.9/test/compare_sam.pl
htslib-1.9/test/cross_validate.sh
htslib-1.9/test/faidx.fa
htslib-1.9/test/fastqs.fq
htslib-1.9/test/fastqs_README.txt
htslib-1.9/test/fieldarith.c
htslib-1.9/test/fieldarith.sam
htslib-1.9/test/formatcols.vcf
htslib-1.9/test/formatmissing-out.vcf
htslib-1.9/test/formatmissing.vcf
htslib-1.9/test/hfile.c
htslib-1.9/test/hts_endian.c
htslib-1.9/test/md#1.sam
htslib-1.9/test/md.fa
htslib-1.9/test/md.fa.fai
htslib-1.9/test/noroundtrip-out.vcf
htslib-1.9/test/noroundtrip.vcf
htslib-1.9/test/range.bam
htslib-1.9/test/range.bam.bai
htslib-1.9/test/range.cram
htslib-1.9/test/range.cram.crai
htslib-1.9/test/range.out
htslib-1.9/test/realn01.fa
htslib-1.9/test/realn01.fa.fai
htslib-1.9/test/realn01.sam
htslib-1.9/test/realn01_exp-a.sam
htslib-1.9/test/realn01_exp-e.sam
htslib-1.9/test/realn01_exp.sam
htslib-1.9/test/realn02-r.sam
htslib-1.9/test/realn02.fa
htslib-1.9/test/realn02.fa.fai
htslib-1.9/test/realn02.sam
htslib-1.9/test/realn02_exp-a.sam
htslib-1.9/test/realn02_exp-e.sam
htslib-1.9/test/realn02_exp.sam
htslib-1.9/test/sam.c
htslib-1.9/test/tabix/
htslib-1.9/test/tabix/bed_file.Y.100200.out
htslib-1.9/test/tabix/bed_file.bed
htslib-1.9/test/tabix/gff_file.X.2934832.2935190.out
htslib-1.9/test/tabix/gff_file.gff
htslib-1.9/test/tabix/large_chr.20.1.2147483647.out
htslib-1.9/test/tabix/large_chr.vcf
htslib-1.9/test/tabix/tabix.tst
htslib-1.9/test/tabix/test-tabix.sh
htslib-1.9/test/tabix/vcf_file.1.3000151.out
htslib-1.9/test/tabix/vcf_file.2.3199812.out
htslib-1.9/test/tabix/vcf_file.vcf
htslib-1.9/test/test-bcf-sr.c
htslib-1.9/test/test-bcf-sr.pl
htslib-1.9/test/test-bcf-translate.c
htslib-1.9/test/test-bcf-translate.out
htslib-1.9/test/test-logging.pl
htslib-1.9/test/test-regidx.c
htslib-1.9/test/test-vcf-api.c
htslib-1.9/test/test-vcf-api.out
htslib-1.9/test/test-vcf-hdr-in.vcf
htslib-1.9/test/test-vcf-hdr.out
htslib-1.9/test/test-vcf-sweep.c
htslib-1.9/test/test-vcf-sweep.out
htslib-1.9/test/test.pl
htslib-1.9/test/test_bgzf.c
htslib-1.9/test/test_realn.c
htslib-1.9/test/test_view.c
htslib-1.9/test/thrash_threads1.c
htslib-1.9/test/thrash_threads2.c
htslib-1.9/test/thrash_threads3.c
htslib-1.9/test/thrash_threads4.c
htslib-1.9/test/thrash_threads5.c
htslib-1.9/test/thrash_threads6.c
htslib-1.9/test/thread_pool.md
htslib-1.9/test/xx#blank.sam
htslib-1.9/test/xx#large_aux.sam
htslib-1.9/test/xx#large_aux2.sam
htslib-1.9/test/xx#large_aux_java.cram
htslib-1.9/test/xx#minimal.sam
htslib-1.9/test/xx#pair.sam
htslib-1.9/test/xx#repeated.sam
htslib-1.9/test/xx#rg.sam
htslib-1.9/test/xx#tlen.sam
htslib-1.9/test/xx#tlen2.sam
htslib-1.9/test/xx#triplet.sam
htslib-1.9/test/xx#unsorted.sam
htslib-1.9/test/xx.fa
htslib-1.9/test/xx.fa.fai
htslib-1.9/textutils.c
htslib-1.9/textutils_internal.h
htslib-1.9/thread_pool.c
htslib-1.9/thread_pool_internal.h
htslib-1.9/vcf.5
htslib-1.9/vcf.c
htslib-1.9/vcf_sweep.c
htslib-1.9/vcfutils.c
htslib-1.9/version.sh
htslib-1.9/config.h.in
htslib-1.9/configure
➜ Tools git:(master) ✗ cd htslib-1.9
➜ htslib-1.9 git:(master) ✗ ls
bcf_sr_sort.c hfile_internal.h knetfile.c sam.c
bcf_sr_sort.h hfile_libcurl.c kstring.c synced_bcf_reader.c
bgzf.c hfile_net.c LICENSE tabix.1
bgzip.1 hfile_s3.c m4 tabix.c
bgzip.c hts.c Makefile tbx.c
config.h.in htsfile.1 md5.c test
config.mk.in htsfile.c multipart.c textutils.c
configure hts_internal.h NEWS textutils_internal.h
configure.ac htslib os thread_pool.c
cram htslib.mk plugin.c thread_pool_internal.h
errmod.c htslib.pc.in probaln.c vcf.5
faidx.5 htslib_vars.mk README vcf.c
faidx.c hts_os.c realn.c vcf_sweep.c
hfile.c INSTALL regidx.c vcfutils.c
hfile_gcs.c kfunc.c sam.5 version.sh
➜ htslib-1.9 git:(master) ✗ make
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#define HAVE_LZMA_H 1' >> config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c
gcc -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -I. -c -o errmod.o errmod.c
gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c
gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9"' > version.h
gcc -g -Wall -O2 -I. -c -o hts.o hts.c
gcc -g -Wall -O2 -I. -c -o hts_os.o hts_os.c
gcc -g -Wall -O2 -I. -c -o md5.o md5.c
gcc -g -Wall -O2 -I. -c -o multipart.o multipart.c
gcc -g -Wall -O2 -I. -c -o probaln.o probaln.c
gcc -g -Wall -O2 -I. -c -o realn.o realn.c
gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c
gcc -g -Wall -O2 -I. -c -o sam.o sam.c
gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I. -c -o textutils.o textutils.c
gcc -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c
gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -I. -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c
gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
ranlib libhts.a
gcc -g -Wall -O2 -I. -fpic -c -o kfunc.pico kfunc.c
gcc -g -Wall -O2 -I. -fpic -c -o knetfile.pico knetfile.c
gcc -g -Wall -O2 -I. -fpic -c -o kstring.pico kstring.c
gcc -g -Wall -O2 -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -Wall -O2 -I. -fpic -c -o bgzf.pico bgzf.c
gcc -g -Wall -O2 -I. -fpic -c -o errmod.pico errmod.c
gcc -g -Wall -O2 -I. -fpic -c -o faidx.pico faidx.c
gcc -g -Wall -O2 -I. -fpic -c -o hfile.pico hfile.c
gcc -g -Wall -O2 -I. -fpic -c -o hfile_net.pico hfile_net.c
gcc -g -Wall -O2 -I. -fpic -c -o hts.pico hts.c
gcc -g -Wall -O2 -I. -fpic -c -o hts_os.pico hts_os.c
gcc -g -Wall -O2 -I. -fpic -c -o md5.pico md5.c
gcc -g -Wall -O2 -I. -fpic -c -o multipart.pico multipart.c
gcc -g -Wall -O2 -I. -fpic -c -o probaln.pico probaln.c
gcc -g -Wall -O2 -I. -fpic -c -o realn.pico realn.c
gcc -g -Wall -O2 -I. -fpic -c -o regidx.pico regidx.c
gcc -g -Wall -O2 -I. -fpic -c -o sam.pico sam.c
gcc -g -Wall -O2 -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -Wall -O2 -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -Wall -O2 -I. -fpic -c -o tbx.pico tbx.c
gcc -g -Wall -O2 -I. -fpic -c -o textutils.pico textutils.c
gcc -g -Wall -O2 -I. -fpic -c -o thread_pool.pico thread_pool.c
gcc -g -Wall -O2 -I. -fpic -c -o vcf.pico vcf.c
gcc -g -Wall -O2 -I. -fpic -c -o vcfutils.pico vcfutils.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/files.pico cram/files.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -shared -Wl,-soname,libhts.so.2 -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -lz -lm -lbz2 -llzma -lpthread
ln -sf libhts.so libhts.so.2
gcc -g -Wall -O2 -I. -c -o bgzip.o bgzip.c
gcc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o htsfile.o htsfile.c
gcc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o tabix.o tabix.c
gcc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o test/hts_endian.o test/hts_endian.c
gcc -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma
gcc -g -Wall -O2 -I. -c -o test/fieldarith.o test/fieldarith.c
gcc -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o test/hfile.o test/hfile.c
gcc -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o test/sam.o test/sam.c
gcc -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c
gcc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_realn.o test/test_realn.c
gcc -o test/test_realn test/test_realn.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-regidx.o test/test-regidx.c
gcc -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_view.o test/test_view.c
gcc -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
